API for paleotree
Paleontological and Phylogenetic Analyses of Evolution
| Global functions | |
|---|---|
| DiversityCurves | Man page |
| HurlbertPIE | Man page Source code |
| PIE | Man page |
| ProbabilityInterspecificEncounter | Man page |
| RaiaCopesRule | Man page |
| SamplingConv | Man page |
| Sankoff_character | Source code |
| SongZhangDicrano | Man page |
| `parLower<-.constrained` | Source code |
| `parLower<-.paleotreeFunc` | Source code |
| `parLower<-` | Source code |
| `parUpper<-.constrained` | Source code |
| `parUpper<-.paleotreeFunc` | Source code |
| `parUpper<-` | Source code |
| `parbounds<-.constrained` | Source code |
| `parbounds<-.paleotreeFunc` | Source code |
| `parbounds<-` | Source code |
| `parnames<-.constrained` | Source code |
| `parnames<-.paleotreeFunc` | Source code |
| `parnames<-` | Source code |
| accioBestAcquisitionModel | Man page Source code |
| accioExhaustionCurve | Man page Source code |
| accio_branch_order_with_stratigraphy | Source code |
| accio_data_from_nexus_file | Source code |
| accio_matrix_tree_from_ape_tree | Source code |
| accio_matrix_tree_from_vector_tree | Source code |
| accio_max_zipf_decay | Source code |
| accio_min_and_max_lognormal_mag_given_hS | Source code |
| accio_minimum_alpha_for_gamma_one | Source code |
| accio_minimum_steps_history | Source code |
| accio_patristic_distance_from_base | Source code |
| addTermBranchLength | Man page Source code |
| ammoniteTraitsRaia | Man page |
| ammoniteTreeRaia | Man page |
| anagEvent | Source code |
| ancPropStateMat | Man page Source code |
| bifurcEvent | Source code |
| binTimeData | Man page Source code |
| bin_cal3TimePaleoPhy | Man page Source code |
| bin_timePaleoPhy | Man page Source code |
| bindPaleoTip | Man page Source code |
| branchClasses | Man page Source code |
| buddingEvent | Source code |
| buildContrastPoly | Source code |
| cal3 | Man page |
| cal3TimePaleoPhy | Man page Source code |
| canConnectPBDB | Source code |
| candleTaxa | Man page |
| ceratopsianTreeRaia | Man page |
| cervidTreeRaia | Man page |
| charEdge2numeric | Source code |
| charExhaustPlot | Man page Source code |
| charMatDicrano | Man page |
| checkFossilRecord | Source code |
| checkRecordForNoDatePastZero | Source code |
| checkRootTime | Source code |
| cladogeneticTraitCont | Man page Source code |
| cladogramDicranoX12 | Man page |
| cladogramDicranoX13 | Man page |
| cleanNewPhylo | Man page Source code |
| cleanTree | Man page |
| collapseNodes | Man page Source code |
| communityEcology | Man page |
| compareNodeAges | Man page Source code |
| compareTermBranches | Man page Source code |
| compareTimescaling | Man page |
| constrainParPaleo | Man page Source code |
| constrainParsePaleo | Source code |
| constructParentChildMatrixPBDB | Source code |
| contiguousIntegerSeq | Source code |
| convertColor2Hex | Source code |
| convertParentChildMatNames | Source code |
| convert_letter_state_to_numeric | Source code |
| createMrBayesConstraints | Man page Source code |
| createMrBayesTipCalibrations | Man page Source code |
| createMrBayesTipDatingNexus | Man page Source code |
| create_quantile_vector | Source code |
| crypticEvent | Source code |
| dateNodes | Man page Source code |
| dateTaxonTreePBDB | Man page Source code |
| date_taxa_on_tree_simple | Source code |
| deadTree | Man page Source code |
| degradeTree | Man page Source code |
| depthRainbow | Man page Source code |
| distribution_loglikelihood_mul | Source code |
| divCurveFossilRecordSim | Man page Source code |
| draw_symmetric_axes | Source code |
| dropExtant | Man page Source code |
| dropExtinct | Man page Source code |
| dropPaleoTip | Man page Source code |
| dropZLB | Man page Source code |
| durationFreq | Man page |
| equation2function | Man page Source code |
| eventOccurs | Source code |
| exhaustionFunctions | Man page |
| expandConstrainForm | Source code |
| expandTaxonTree | Man page Source code |
| expected_abundances | Source code |
| expected_exhaustion_curve | Source code |
| expected_sampled_richness | Source code |
| expected_sampling_curve | Source code |
| extEvent | Source code |
| findNoParentMatch | Source code |
| fisher_plot | Source code |
| fixRootTime | Man page Source code |
| fixSelfParents | Source code |
| footeValues | Man page Source code |
| foramAL | Man page |
| foramALb | Man page |
| foramAM | Man page |
| foramAMb | Man page |
| fossilRecord2fossilRanges | Man page Source code |
| fossilRecord2fossilTaxa | Man page Source code |
| fossilTaxa2fossilRecord | Man page Source code |
| fourDate2timeList | Man page Source code |
| fourDateFunctions | Man page |
| freqRat | Man page Source code |
| gamma_distribution | Source code |
| geometric_distribution | Source code |
| getAllParents | Source code |
| getCladeTaxaPBDB | Man page Source code |
| getCoordsPhyloPic | Source code |
| getDataPBDB | Man page |
| getFloatAncPBDB | Source code |
| getLinneanTaxonTreePBDB | Source code |
| getMrBFixedAgesFromNexus | Source code |
| getPBDBocc | Man page Source code |
| getPBDBtaxaCSV | Source code |
| getPhyloPicFromPhyloPic | Source code |
| getPhyloPicIDNumFromPBDB | Source code |
| getPhyloPicPNG | Source code |
| getPhyloPicPNG_PBDB | Source code |
| getPhyloPicUIDsTableFromPBDB | Source code |
| getPosteriorProbabiities | Source code |
| getRateMatrix | Source code |
| getRootID | Source code |
| getRunVitals | Source code |
| getSortedMinMaxStratRanges | Source code |
| getSpecificTaxaPBDB | Man page Source code |
| getTaxRankPBDB | Source code |
| getTaxaNames | Source code |
| getTaxonDurations | Source code |
| getUltimateAnc | Source code |
| graptCharMatrix | Man page |
| graptDisparity | Man page |
| graptDistMat | Man page |
| graptOccPBDB | Man page |
| graptPBDB | Man page |
| graptRanges | Man page |
| graptTaxaPBDB | Man page |
| graptTimeTree | Man page |
| graptTree | Man page |
| horizonSampRate | Man page Source code |
| initiateTaxa | Source code |
| insertRow | Source code |
| invSurv | Man page |
| inverseSurv | Man page |
| isTimeListSequential | Source code |
| jack5_Fisher | Source code |
| kanto | Man page |
| loglikelihood_gamma_one_rad | Source code |
| loglikelihood_geometric_rad | Source code |
| loglikelihood_lognormal_rad | Source code |
| loglikelihood_lognormal_rad_for_optim | Source code |
| loglikelihood_zipf_rad | Source code |
| lognormal_distribution | Source code |
| macroperforateForam | Man page |
| makeEmptyMorphNexusMrB | Source code |
| makeIngroupConstraintMrB | Source code |
| makeMrBayesBlock | Source code |
| makePBDBtaxonTree | Man page Source code |
| makeParFunct | Source code |
| make_durationFreqCont | Man page Source code |
| make_durationFreqDisc | Man page Source code |
| make_inverseSurv | Man page Source code |
| make_paleotreeFunc | Source code |
| matchTaxaColor | Source code |
| minBranchLen | Man page |
| minBranchLength | Man page Source code |
| minCharChange | Man page Source code |
| minimumBranchLen | Man page |
| minimumBranchLength | Man page |
| modelMethods | Man page |
| modified_AIC | Source code |
| modifyTerminalBranches | Man page |
| multiDiv | Man page Source code |
| nContradiction | Source code |
| nearestNeighborDist | Man page Source code |
| newTaxon | Source code |
| nodeDates2branchLengths | Man page Source code |
| obtainDatedPosteriorTreesMrB | Man page Source code |
| occData2timeList | Man page Source code |
| optimPaleo | Man page Source code |
| optimize_gamma_one_abundance | Source code |
| optimize_gamma_one_abundance_given_hS | Source code |
| optimize_geometric_abundance | Source code |
| optimize_lognormal_abundance | Source code |
| optimize_lognormal_abundance_given_hS | Source code |
| optimize_uniform_abundance | Source code |
| optimize_zipf_abundance | Source code |
| optimize_zipf_abundance_given_hS | Source code |
| origination | Source code |
| pairwiseSpearmanRho | Man page Source code |
| paleotree | Man page |
| paleotree-package | Man page |
| parInit | Man page Source code |
| parInit.constrained | Man page Source code |
| parInit.paleotreeFunc | Man page Source code |
| parLower | Man page Source code |
| parLower.constrained | Man page Source code |
| parLower.paleotreeFunc | Man page Source code |
| parLower<- | Man page |
| parLower<-.constrained | Man page |
| parLower<-.paleotreeFunc | Man page |
| parUpper | Man page Source code |
| parUpper.constrained | Man page Source code |
| parUpper.paleotreeFunc | Man page Source code |
| parUpper<- | Man page |
| parUpper<-.constrained | Man page |
| parUpper<-.paleotreeFunc | Man page |
| parbounds | Man page Source code |
| parbounds.constrained | Man page Source code |
| parbounds.paleotreeFunc | Man page Source code |
| parbounds<- | Man page |
| parbounds<-.constrained | Man page |
| parbounds<-.paleotreeFunc | Man page |
| parentChild2taxonTree | Man page Source code |
| parentChildPBDBOld | Source code |
| parnames | Man page Source code |
| parnames.constrained | Man page Source code |
| parnames.paleotreeFunc | Man page Source code |
| parnames<- | Man page |
| parnames<-.constrained | Man page |
| parnames<-.paleotreeFunc | Man page |
| parseNexusFile | Source code |
| parseParentPBDBData | Source code |
| perCapitaRates | Man page Source code |
| perfectParsCharTree | Man page Source code |
| phyloDiv | Man page Source code |
| plotMultiDiv | Man page Source code |
| plotOccData | Man page Source code |
| plotPhyloPicTree | Man page Source code |
| plotSinglePhyloPic | Source code |
| plotTaxaTreePBDB | Man page Source code |
| plotTaxonStratDurations | Source code |
| plotTraitgram | Man page Source code |
| pqr2Ps | Man page Source code |
| pqsRate2sProb | Man page Source code |
| prepPhyloPic | Source code |
| probAnc | Man page Source code |
| processTaxonAppData | Source code |
| pullOccListData | Source code |
| qsProb2Comp | Man page Source code |
| qsRate2Comp | Man page Source code |
| queryMissingParents | Source code |
| ravel_polymorph | Source code |
| read_nexus_tree | Source code |
| resolveTreeChar | Man page Source code |
| resolveTreeCharMechanism | Source code |
| retioChar | Man page |
| retioRanges | Man page |
| retioTree | Man page |
| retiolitinae | Man page |
| reverseList | Man page Source code |
| rootSplit | Man page Source code |
| sProb2sRate | Man page Source code |
| sRate2sProb | Man page Source code |
| sampEvent | Source code |
| sampleRanges | Man page Source code |
| sampleSeqVitals | Source code |
| seqTimeList | Man page Source code |
| setRootAge | Man page Source code |
| setRootAges | Man page Source code |
| shellSize | Man page |
| simCandleTaxa | Man page |
| simFossilRecord | Man page Source code |
| simFossilRecordMethods | Man page |
| simTermTaxa | Man page Source code |
| simTermTaxaAdvanced | Man page Source code |
| subsetParDataPBDB | Source code |
| sutureComplexity | Man page |
| taxa2cladogram | Man page Source code |
| taxa2phylo | Man page Source code |
| taxicDivCont | Man page Source code |
| taxicDivDisc | Man page Source code |
| taxonSortPBDBocc | Man page Source code |
| taxonTable2taxonTree | Man page Source code |
| termTaxa | Man page |
| termination | Source code |
| testContinue | Source code |
| testContradiction | Source code |
| testEdgeMat | Man page Source code |
| testFinal | Source code |
| testParentChild | Source code |
| testTimeList | Source code |
| testVitalsRecord | Source code |
| timeLadderTree | Man page Source code |
| timeList2fourDate | Man page Source code |
| timePaleoPhy | Man page Source code |
| timeSliceFossilRecord | Man page Source code |
| timeSliceTree | Man page Source code |
| tipDatingCompatabilitySummaryMrB | Man page Source code |
| tipdating | Man page |
| translatePBDBocc | Source code |
| translatePBDBtaxa | Source code |
| treeContradiction | Man page Source code |
| trueCandle | Man page |
| trueTermTaxaTree | Man page Source code |
| twoWayEcologyCluster | Man page Source code |
| unitLengthTree | Man page Source code |
| unravel_polymorph | Source code |
| whichLive | Source code |
| whichSampled | Source code |
| whichSampledInPast | Source code |
| worthCheckingVitalsRecord | Source code |
| writeSimpleSumtNexus | Source code |
| zipf_distribution | Source code |
